rs4958846

chr5-150845576-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.252 in 152,102 control chromosomes in the GnomAD database, including 6,981 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38241 AN: 151986 Hom.: 6961 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.252 AC: 38300 AN: 152102 Hom.: 6981 Cov.: 32 AF XY: 0.253 AC XY: 18808 AN XY: 74356

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.253

Alfa AF: 0.187 Hom.: 495

Bravo AF: 0.270

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.071

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4958846; hg19: chr5-150225138;